Literature DB >> 24495512

Bacterial growth: global effects on gene expression, growth feedback and proteome partition.

Stefan Klumpp1, Terence Hwa2.   

Abstract

The function of endogenous as well as synthetic genetic circuits is generically coupled to the physiological state of the cell. For exponentially growing bacteria, a key characteristic of the state of the cell is the growth rate and thus gene expression is often growth-rate dependent. Here we review recent results on growth-rate dependent gene expression. We distinguish different types of growth-rate dependencies by the mechanisms of regulation involved and the presence or absence of an effect of the gene product on growth. The latter can lead to growth feedback, feedback mediated by changes of the global state of the cell. Moreover, we discuss how growth rate dependence can be used as a guide to study the molecular implementation of physiological regulation.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 24495512      PMCID: PMC4111964          DOI: 10.1016/j.copbio.2014.01.001

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  52 in total

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Authors:  Nathalie Q Balaban; Jack Merrin; Remy Chait; Lukasz Kowalik; Stanislas Leibler
Journal:  Science       Date:  2004-08-12       Impact factor: 47.728

2.  Interdependence of cell growth and gene expression: origins and consequences.

Authors:  Matthew Scott; Carl W Gunderson; Eduard M Mateescu; Zhongge Zhang; Terence Hwa
Journal:  Science       Date:  2010-11-19       Impact factor: 47.728

3.  Five hard truths for synthetic biology.

Authors:  Roberta Kwok
Journal:  Nature       Date:  2010-01-21       Impact factor: 49.962

4.  Physiological regulation of a decontrolled lac operon.

Authors:  B L Wanner; R Kodaira; F C Neidhardt
Journal:  J Bacteriol       Date:  1977-04       Impact factor: 3.490

Review 5.  Bacterial persistence and toxin-antitoxin loci.

Authors:  Kenn Gerdes; Etienne Maisonneuve
Journal:  Annu Rev Microbiol       Date:  2012       Impact factor: 15.500

6.  ppGpp is the major source of growth rate control in E. coli.

Authors:  Katarzyna Potrykus; Helen Murphy; Nadège Philippe; Michael Cashel
Journal:  Environ Microbiol       Date:  2010-10-15       Impact factor: 5.491

7.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Authors:  J S Edwards; R U Ibarra; B O Palsson
Journal:  Nat Biotechnol       Date:  2001-02       Impact factor: 54.908

8.  Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction.

Authors:  H Dong; L Nilsson; C G Kurland
Journal:  J Bacteriol       Date:  1995-03       Impact factor: 3.490

9.  Growth-rate dependence reveals design principles of plasmid copy number control.

Authors:  Stefan Klumpp
Journal:  PLoS One       Date:  2011-05-27       Impact factor: 3.240

10.  Dilution and the theoretical description of growth-rate dependent gene expression.

Authors:  Marius Hintsche; Stefan Klumpp
Journal:  J Biol Eng       Date:  2013-09-16       Impact factor: 4.355

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  65 in total

1.  Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.

Authors:  Peter L Freddolino; Jamie Yang; Amir Momen-Roknabadi; Saeed Tavazoie
Journal:  Elife       Date:  2018-04-05       Impact factor: 8.140

2.  Prevalence of antiseptic resistance genes increases in staphylococcal isolates from orthokeratology lens wearers over initial six-month period of use.

Authors:  Shi Guang-Sen; Maureen Boost; Pauline Cho
Journal:  Eur J Clin Microbiol Infect Dis       Date:  2016-03-18       Impact factor: 3.267

3.  Temporal encoding of bacterial identity and traits in growth dynamics.

Authors:  Carolyn Zhang; Wenchen Song; Helena R Ma; Xiao Peng; Deverick J Anderson; Vance G Fowler; Joshua T Thaden; Minfeng Xiao; Lingchong You
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-03       Impact factor: 11.205

4.  Statistical Package for Growth Rates Made Easy.

Authors:  Portia Mira; Miriam Barlow; Juan C Meza; Barry G Hall
Journal:  Mol Biol Evol       Date:  2017-12-01       Impact factor: 16.240

Review 5.  Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review.

Authors:  Suckjoon Jun; Fangwei Si; Rami Pugatch; Matthew Scott
Journal:  Rep Prog Phys       Date:  2018-01-09

6.  Robust, linear correlations between growth rates and β-lactam-mediated lysis rates.

Authors:  Anna J Lee; Shangying Wang; Hannah R Meredith; Bihan Zhuang; Zhuojun Dai; Lingchong You
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-02       Impact factor: 11.205

7.  Simulating Genetic Circuits in Bacterial Populations with Growth Heterogeneity.

Authors:  Anjan Roy; Stefan Klumpp
Journal:  Biophys J       Date:  2018-01-23       Impact factor: 4.033

Review 8.  How to deal with parameters for whole-cell modelling.

Authors:  Ann C Babtie; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2017-08-02       Impact factor: 4.118

Review 9.  The Biosynthetic Basis of Cell Size Control.

Authors:  Kurt M Schmoller; Jan M Skotheim
Journal:  Trends Cell Biol       Date:  2015-11-10       Impact factor: 20.808

10.  Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.

Authors:  Jose Utrilla; Edward J O'Brien; Ke Chen; Douglas McCloskey; Jacky Cheung; Harris Wang; Dagoberto Armenta-Medina; Adam M Feist; Bernhard O Palsson
Journal:  Cell Syst       Date:  2016-04-27       Impact factor: 10.304

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